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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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Aoki M, Vinokur J, Motoyama K, Ishikawa R, Collazo M, Cascio D, Sawaya MR, Ito T, Bowie JU, Hemmi H. Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways. J Biol Chem 2022; 298:102111. [PMID: 35690147 PMCID: PMC9254496 DOI: 10.1016/j.jbc.2022.102111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/04/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
Mevalonate 3,5-bisphosphate decarboxylase is involved in the recently discovered Thermoplasma-type mevalonate pathway. The enzyme catalyzes the elimination of the 3-phosphate group from mevalonate 3,5-bisphosphate as well as concomitant decarboxylation of the substrate. This entire reaction of the enzyme resembles the latter half-reactions of its homologs, diphosphomevalonate decarboxylase and phosphomevalonate decarboxylase, which also catalyze ATP-dependent phosphorylation of the 3-hydroxyl group of their substrates. However, the crystal structure of mevalonate 3,5-bisphosphate decarboxylase and the structural reasons of the difference between reactions catalyzed by the enzyme and its homologs are unknown. In this study, we determined the X-ray crystal structure of mevalonate 3,5-bisphosphate decarboxylase from Picrophilus torridus, a thermoacidophilic archaeon of the order Thermoplasmatales. Structural and mutational analysis demonstrated the importance of a conserved aspartate residue for enzyme activity. In addition, although crystallization was performed in the absence of substrate or ligands, residual electron density having the shape of a fatty acid was observed at a position overlapping the ATP-binding site of the homologous enzyme, diphosphomevalonate decarboxylase. This finding is in agreement with the expected evolutionary route from phosphomevalonate decarboxylase (ATP-dependent) to mevalonate 3,5-bisphosphate decarboxylase (ATP-independent) through the loss of kinase activity. We found that the binding of geranylgeranyl diphosphate, an intermediate of the archeal isoprenoid biosynthesis pathway, evoked significant activation of mevalonate 3,5-bisphosphate decarboxylase, and several mutations at the putative geranylgeranyl diphosphate-binding site impaired this activation, suggesting the physiological importance of ligand binding as well as a possible novel regulatory system employed by the Thermoplasma-type mevalonate pathway.
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Affiliation(s)
- Mizuki Aoki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan
| | - Jeffrey Vinokur
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Kento Motoyama
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan
| | - Rino Ishikawa
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan
| | - Michael Collazo
- Departments of Biological Chemistry, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Duilio Cascio
- Departments of Biological Chemistry, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Michael R Sawaya
- UCLA-DOE Institute of Genomics and Proteomics, Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Tomokazu Ito
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Hisashi Hemmi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya, Aichi, Japan.
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Eichler J, Guan Z. Lipid sugar carriers at the extremes: The phosphodolichols Archaea use in N-glycosylation. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:589-599. [PMID: 28330764 DOI: 10.1016/j.bbalip.2017.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 11/28/2022]
Abstract
N-glycosylation, a post-translational modification whereby glycans are covalently linked to select Asn residues of target proteins, occurs in all three domains of life. Across evolution, the N-linked glycans are initially assembled on phosphorylated cytoplasmically-oriented polyisoprenoids, with polyprenol (mainly C55 undecaprenol) fulfilling this role in Bacteria and dolichol assuming this function in Eukarya and Archaea. The eukaryal and archaeal versions of dolichol can, however, be distinguished on the basis of their length, degree of saturation and by other traits. As is true for many facets of their biology, Archaea, best known in their capacity as extremophiles, present unique approaches for synthesizing phosphodolichols. At the same time, general insight into the assembly and processing of glycan-bearing phosphodolichols has come from studies of the archaeal enzymes responsible. In this review, these and other aspects of archaeal phosphodolichol biology are addressed.
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Affiliation(s)
- Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 84105, Israel.
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Motoyama K, Unno H, Hattori A, Takaoka T, Ishikita H, Kawaide H, Yoshimura T, Hemmi H. A Single Amino Acid Mutation Converts ( R)-5-Diphosphomevalonate Decarboxylase into a Kinase. J Biol Chem 2016; 292:2457-2469. [PMID: 28003359 DOI: 10.1074/jbc.m116.752535] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/11/2016] [Indexed: 11/06/2022] Open
Abstract
The biosynthesis of isopentenyl diphosphate, a fundamental precursor for isoprenoids, via the mevalonate pathway is completed by diphosphomevalonate decarboxylase. This enzyme catalyzes the formation of isopentenyl diphosphate through the ATP-dependent phosphorylation of the 3-hydroxyl group of (R)-5-diphosphomevalonate followed by decarboxylation coupled with the elimination of the 3-phosphate group. In this reaction, a conserved aspartate residue has been proposed to be involved in the phosphorylation step as the general base catalyst that abstracts a proton from the 3-hydroxyl group. In this study, the catalytic mechanism of this rare type of decarboxylase is re-investigated by structural and mutagenic studies on the enzyme from a thermoacidophilic archaeon Sulfolobus solfataricus The crystal structures of the archaeal enzyme in complex with (R)-5-diphosphomevalonate and adenosine 5'-O-(3-thio)triphosphate or with (R)-5-diphosphomevalonate and ADP are newly solved, and theoretical analysis based on the structure suggests the inability of proton abstraction by the conserved aspartate residue, Asp-281. Site-directed mutagenesis on Asp-281 creates mutants that only show diphosphomevalonate 3-kinase activity, demonstrating that the residue is required in the process of phosphate elimination/decarboxylation, rather than in the preceding phosphorylation step. These results enable discussion of the catalytic roles of the aspartate residue and provide clear proof of the involvement of a long predicted intermediate, (R)-3-phospho-5-diphosphomevalonate, in the reaction of the enzyme.
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Affiliation(s)
- Kento Motoyama
- From the Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601
| | - Hideaki Unno
- the Graduate School of Engineering, Nagasaki University, Bunkyo-machi, Nagasaki, Nagasaki 852-8521
| | - Ai Hattori
- From the Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601
| | - Tomohiro Takaoka
- the Department of Applied Chemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654
| | - Hiroshi Ishikita
- the Department of Applied Chemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654.,the Research Center for Advanced Science and Technology, University of Tokyo, Komaba 4-6-1, Meguro, Tokyo 153-8904, and
| | - Hiroshi Kawaide
- the Institute of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo 183-8509, Japan
| | - Tohru Yoshimura
- From the Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601
| | - Hisashi Hemmi
- From the Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601,
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